Commit 96c2e535 authored by Alexandre Bône's avatar Alexandre Bône

Remove "deformetrica-min-version="3.0.0"".

parent 3d913a03
Pipeline #50174359 failed with stages
in 21 minutes and 3 seconds
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="sub1">
<visit id="t0">
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>DeterministicAtlas</model-type>
<dimension>2</dimension>
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>DeterministicAtlas</model-type>
<dimension>2</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>ScipyLBFGS</optimization-method-type>
<max-iterations>100</max-iterations>
<save-every-n-iters>50</save-every-n-iters>
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="sub_1">
<visit id="experiment">
<filename object_id="img">data/image2.png</filename>
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>DeterministicAtlas</model-type>
<dimension>2</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>GradientAscent</optimization-method-type>
<save-every-n-iters>10</save-every-n-iters>
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="australopithecus">
<visit id="experiment">
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>DeterministicAtlas</model-type>
<!-- <model-type>BayesianAtlas</model-type> -->
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>GradientAscent</optimization-method-type>
<!--<optimization-method-type>ScipyLBFGS</optimization-method-type>-->
<use-sobolev-gradient>On</use-sobolev-gradient>
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="subj1">
<visit id="experiment">
<filename object_id="amygdala">data/amygdala1.vtk</filename>
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>DeterministicAtlas</model-type>
<dimension>3</dimension>
<template>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>GradientAscent</optimization-method-type>
<initial-step-size>0.01</initial-step-size>
<max-iterations>20</max-iterations>
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="s0">
<visit id="t11">
......
<?xml version="1.0" ?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>LongitudinalAtlas</model-type>
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>LongitudinalAtlas</model-type>
<dimension>2</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>McmcSaem</optimization-method-type>
......
<?xml version="1.0" ?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="s0041">
<visit id="v0">
<age>71.10</age>
......
<?xml version="1.0" ?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>LongitudinalAtlas</model-type>
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>LongitudinalAtlas</model-type>
<dimension>3</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>McmcSaem</optimization-method-type>
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="s0">
<visit id="t0">
......
<?xml version="1.0" ?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>LongitudinalAtlas</model-type>
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>LongitudinalAtlas</model-type>
<dimension>2</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>McmcSaem</optimization-method-type>
<!--<optimization-method-type>ScipyLBFGS</optimization-method-type>-->
......
<?xml version="1.0" ?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>LongitudinalRegistration</model-type>
......
<?xml version="1.0" ?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>LongitudinalAtlas</model-type>
<dimension>2</dimension>
......
<?xml version="1.0" ?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>LongitudinalRegistration</model-type>
<dimension>2</dimension>
......
<?xml version="1.0" ?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>LongitudinalRegistration</model-type>
<dimension>2</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>ScipyPowell</optimization-method-type>
<!--<optimization-method-type>ScipyLBFGS</optimization-method-type>-->
......
<?xml version="1.0" ?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="sub-ADNI002S0729">
<visit id="ses-M00">
<age>65.10</age>
......
<?xml version="1.0" ?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="sub-ADNI002S0729">
<visit id="ses-M00">
<age>65.10</age>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>McmcSaem</optimization-method-type>
......
<?xml version="1.0" ?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>LongitudinalAtlas</model-type>
<dimension>3</dimension>
......
<?xml version="1.0" ?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>LongitudinalAtlas</model-type>
<dimension>3</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<!--<optimization-method-type>ScipyPowell</optimization-method-type>-->
<!-- <optimization-method-type>ScipyLBFGS</optimization-method-type>-->
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="s0">
<visit id="t0">
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>LongitudinalRegistration</model-type>
<dimension>2</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<!--<optimization-method-type>ScipyPowell</optimization-method-type>-->
<!--<optimization-method-type>ScipyLBFGS</optimization-method-type>-->
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="image">
<visit id="experiment">
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>ParallelTransport</model-type>
<dimension>2</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
</optimization-parameters>
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="1">
<visit id="experiment">
<filename object_id="digit">data/digit_2_sample_30.png</filename>
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>Registration</model-type>
<template>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>GradientAscent</optimization-method-type>
<initial-step-size>1e-2</initial-step-size>
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="image">
<visit id="experiment">
<filename object_id="img">data/I3.png</filename>
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>Registration</model-type>
<dimension>2</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>GradientAscent</optimization-method-type>
<initial-step-size>1e-1</initial-step-size>
<save-every-n-iters>10</save-every-n-iters>
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="image">
<visit id="experiment">
<filename object_id="img">data/image2.png</filename>
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>Registration</model-type>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>GradientAscent</optimization-method-type>
<optimize-initial-cp>On</optimize-initial-cp>
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="target">
<visit id="baseline">
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>DeterministicAtlas</model-type>
<dimension>2</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>GradientAscent</optimization-method-type>
<!--<optimization-method-type>ScipyLBFGS</optimization-method-type>-->
......
<?xml version="1.0" ?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="target">
<visit id="v0">
<filename object_id="brain">data/s0021_7960_8.nii</filename>
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>DeterministicAtlas</model-type>
<dimension>3</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>ScipyLBFGS</optimization-method-type>
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="target">
<visit id="target">
<filename object_id="pointcloud">data/targetPoints.vtk</filename>
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>Registration</model-type>
<dimension>2</dimension>
<template>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>GradientAscent</optimization-method-type>
<initial-step-size>1e-8</initial-step-size>
<freeze-template>On</freeze-template>
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="starfish">
<visit id="baseline">
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>Registration</model-type>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>GradientAscent</optimization-method-type>
<initial-step-size>1e-3</initial-step-size>
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="subj1">
<visit id="experiment">
<filename object_id="bundle">data/subject_bundle.vtk</filename>
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>Registration</model-type>
<template>
<object id="bundle">
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>GradientAscent</optimization-method-type>
<initial-step-size>1e-5</initial-step-size>
</optimization-parameters>
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="sub1">
<visit id="t-5">
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>Regression</model-type>
<dimension>2</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>GradientAscent</optimization-method-type>
<max-iterations>50</max-iterations>
<save-every-n-iters>5</save-every-n-iters>
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="evolution">
<visit id="australopithecus">
<age>1</age>
......
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>Regression</model-type>
<dimension>2</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<optimization-method-type>GradientAscent</optimization-method-type>
<max-iterations>100</max-iterations>
<save-every-n-iters>10</save-every-n-iters>
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
</data-set>
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>Shooting</model-type>
<dimension>2</dimension>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
</optimization-parameters>
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
</data-set>
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>Shooting</model-type>
<initial-control-points>data/INITIALISATIONCP.txt</initial-control-points>
<initial-momenta>data/INITIALISATIONMOM.txt</initial-momenta>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
</optimization-parameters>
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
</data-set>
<?xml version="1.0"?>
<model deformetrica-min-version="3.0.0">
<model>
<model-type>Shooting</model-type>
<dimension>3</dimension>
<template>
......
<?xml version="1.0"?>
<optimization-parameters deformetrica-min-version="3.0.0">
<optimization-parameters>
<!-- <optimization-method-type>TorchLBFGS</optimization-method-type> -->
<!-- <optimization-method-type>GradientAscent</optimization-method-type> -->
......
......@@ -515,7 +515,7 @@ class XmlParameters:
'acceleration and multithreading. Overriding the "number-of-threads" option, now set to 1.'
warnings.warn(msg)
elif self.model_type in ['BayesianAtlas'.lower(), 'GeodesicRegression'.lower(), 'Shooting'.lower()]:
elif self.model_type in ['BayesianAtlas'.lower(), 'Regression'.lower(), 'Shooting'.lower()]:
self.number_of_threads = 1
msg = 'It is not possible at the moment to estimate a "%s" model with multithreading. ' \
'Overriding the "number-of-threads" option, now set to 1.' % self.model_type
......
<?xml version="1.0"?>
<data-set deformetrica-min-version="3.0.0">
<data-set>
<subject id="subj1">
<visit id="experiment">
<filename object_id="amygdala">data/amygdala1_decimated.vtk</filename>
......